Spatial Heterogeneity of Fecal Indicator Bacteria and Salmonella enterica in the Tagus and Sado Estuaries: A Short-Term Monitoring Study with Antimicrobial Susceptibility Profiling

Estuaries receive microbial inputs from multiple sources, but short-term monitoring may conceal marked local heterogeneity. We assessed fecal indicator bacteria (FIB), Salmonella enterica occurrence, and antimicrobial susceptibility in the Tagus and Sado estuaries, Portugal. Thirty-six surface-water samples were collected at six sites during six campaigns between 1 May and 25 June 2025 and analysed using ISO-based culture methods. FIB concentrations differed significantly among sites for Escherichia coli (Friedman χ2 = 23.905, p < 0.001, Kendall’s W = 0.797), total coliforms (χ2 = 21.333, p < 0.001, W = 0.711), and intestinal enterococci (χ2 = 24.234, p < 0.001, W = 0.808), whereas paired estuary-level campaign means did not differ significantly. FIB were strongly correlated, and PCA identified a dominant contamination gradient (PC1 = 86.7%). Salmonella enterica was recovered from 10/36 samples (27.8%) across five sites; positive samples had higher FIB concentrations in exploratory Holm-adjusted analyses. Eight Salmonella isolates had no recorded antimicrobial resistance within the tested panel, whereas two displayed multidrug-resistant phenotypes. These findings support spatially resolved surveillance while the short sampling window precludes seasonal or annual inference.